Additional file 1 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

Tables S1-S15. Microsoft Excel Workbook containing 15 worksheets. Table S1: Description of Pst isolates. Table S2: Number of reads aligned to the PST-130 reference genome for the 100 RNA-seq datasets. Table S3: Number of reads aligned to the PST-130 reference genome for the 25 genomic datasets utilised herein. Table S4: Oligonucleotide (primer) sequences and pooling strategy for the 242 Pst genes selected. Table S5: Genomic location and functional annotation of the 242 Pst genes selected. Table S6: Number of reads aligned to the PST-130 reference genome for the 4 MiSeq amplicon datasets. Table S7: Number of reads generated on the MinION platform that aligned to the 242 Pst genes selected. Table S8: Time taken to generate a given number of MinION reads for the four Ethiopian Pst-infected wheat samples. Table S9: Details of SNP positions per gene detected in MinION and Illumina datasets generated from four Pst isolates. Table S10: Details of homokaryotic and heterokaryotic positions in consensus sequences obtained from Illumina MiSeq and MinION platforms. Table S11: Number of reads aligned to the PST-130 reference genome for the Ethiopian Pst RNA-seq datasets. Table S12: Additional Pst reference isolates representing diverse virulence phenotypes and key genetic groups of a worldwide phylogeny of Pst. Table S13: Components used in the MARPLE pipeline. Table S14: Details of Illumina library preparation of 4 Pst-infected samples. Table S15: Details of libraries made for MinION sequencing of Pst-infected wheat leaf samples. (XLSX 4138 kb)

附表S1至S15：包含15个工作表的Microsoft Excel工作簿。
附表S1：Pst分离株概况
附表S2：100套RNA-seq数据集的读段（reads）比对至PST-130参考基因组的数量
附表S3：本研究使用的25套基因组测序数据集的读段（reads）比对至PST-130参考基因组的数量
附表S4：筛选得到的242个Pst基因的寡核苷酸（引物）序列及混合方案
附表S5：筛选得到的242个Pst基因的基因组定位与功能注释
附表S6：4套MiSeq扩增子测序数据集的读段（reads）比对至PST-130参考基因组的数量
附表S7：MinION平台产出的、比对至筛选得到的242个Pst基因的读段（reads）数量
附表S8：4份埃塞俄比亚感染Pst的小麦样本生成指定数量MinION读段所需的时长
附表S9：从4株Pst分离株获得的MinION与Illumina测序数据中，每个基因的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点详情
附表S10：从Illumina MiSeq与MinION平台获得的共识序列中，同核与异核位点详情
附表S11：埃塞俄比亚Pst RNA-seq数据集的读段（reads）比对至PST-130参考基因组的数量
附表S12：代表全球Pst系统发育树中多样毒力表型与关键遗传类群的补充Pst参考分离株
附表S13：MARPLE分析流程所用的组件
附表S14：4份感染Pst的样本的Illumina文库制备详情
附表S15：针对感染Pst的小麦叶片样本开展MinION测序所用的文库构建详情
（XLSX格式，文件大小4138千字节）